Pathway analysis in metabolomics: Recommendations for the use of over-representation analysis (Q111803756)

2 May 2022

Juliette Cooke

ORCID iD

0000-0003-2085-0339

series ordinal

6

1 reference

2 May 2022

Rachel PJ Lai

ORCID iD

0000-0003-3418-850X

series ordinal

7

1 reference

2 May 2022

Timothy Ebbels

series ordinal

10

1 reference

PLOS Computational Biology

2 May 2022

language of work or name

1 reference

2 May 2022

7 September 2021

1 reference

2 May 2022

1 reference

2 May 2022

17

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2 May 2022

e1009105

1 reference

2 May 2022

9

1 reference

2 May 2022

Creative Commons Attribution 4.0 International

start time

7 September 2021

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April 2022 Public Data File from Crossref

copyright status

copyrighted

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cites work

High-fat diet fuels prostate cancer progression by rewiring the metabolome and amplifying the MYC program

1 reference

https://opencitations.net/index/coci/api/v1/references/10.1371/JOURNAL.PCBI.1009105

Systematic determination of genetic network architecture

3 May 2022

1 reference

https://opencitations.net/index/coci/api/v1/references/10.1371/JOURNAL.PCBI.1009105

3 May 2022

1 reference

https://opencitations.net/index/coci/api/v1/references/10.1371/JOURNAL.PCBI.1009105

BioServices: a common Python package to access biological Web Services programmatically

3 May 2022

1 reference

https://opencitations.net/index/coci/api/v1/references/10.1371/JOURNAL.PCBI.1009105

Causal analysis approaches in Ingenuity Pathway Analysis

3 May 2022

1 reference

https://opencitations.net/index/coci/api/v1/references/10.1371/JOURNAL.PCBI.1009105

Serum metabolomic profiles associated with postmenopausal hormone use

3 May 2022

1 reference

https://opencitations.net/index/coci/api/v1/references/10.1371/JOURNAL.PCBI.1009105

Mind the Gap: Mapping Mass Spectral Databases in Genome-Scale Metabolic Networks Reveals Poorly Covered Areas

3 May 2022

2 references

https://opencitations.net/index/coci/api/v1/references/10.1371/JOURNAL.PCBI.1009105

3 May 2022

3 May 2022

https://opencitations.net/index/coci/api/v1/citations/10.3390/METABO8030051

The BioCyc collection of microbial genomes and metabolic pathways.

1 reference

https://opencitations.net/index/coci/api/v1/references/10.1371/JOURNAL.PCBI.1009105

Consistency, Inconsistency, and Ambiguity of Metabolite Names in Biochemical Databases Used for Genome-Scale Metabolic Modelling

3 May 2022

1 reference

https://opencitations.net/index/coci/api/v1/references/10.1371/JOURNAL.PCBI.1009105

Relationships between digestive efficiency and metabolomic profiles of serum and intestinal contents in chickens.

3 May 2022

1 reference

https://opencitations.net/index/coci/api/v1/references/10.1371/JOURNAL.PCBI.1009105

Transcriptomic and metabolomic data integration

3 May 2022

1 reference

https://opencitations.net/index/coci/api/v1/references/10.1371/JOURNAL.PCBI.1009105

iPath3.0: interactive pathways explorer v3.

3 May 2022

1 reference

https://opencitations.net/index/coci/api/v1/references/10.1371/JOURNAL.PCBI.1009105

MetaboAnalyst 4.0: towards more transparent and integrative metabolomics analysis.

3 May 2022

1 reference

https://opencitations.net/index/coci/api/v1/references/10.1371/JOURNAL.PCBI.1009105

Critical assessment of human metabolic pathway databases: a stepping stone for future integration

3 May 2022

1 reference

https://opencitations.net/index/coci/api/v1/references/10.1371/JOURNAL.PCBI.1009105

Ranking Metabolite Sets by Their Activity Levels

3 May 2022

2 references

https://opencitations.net/index/coci/api/v1/references/10.1371/JOURNAL.PCBI.1009105

3 May 2022

https://opencitations.net/index/coci/api/v1/citations/10.3390/METABO11020103

PathMe: merging and exploring mechanistic pathway knowledge

3 May 2022

1 reference

https://opencitations.net/index/coci/api/v1/references/10.1371/JOURNAL.PCBI.1009105

The Impact of Pathway Database Choice on Statistical Enrichment Analysis and Predictive Modeling

3 May 2022

1 reference

https://opencitations.net/index/coci/api/v1/references/10.1371/JOURNAL.PCBI.1009105

Erratum: Publisher Correction: ComPath: an ecosystem for exploring, analyzing, and curating mappings across pathway databases

3 May 2022

1 reference

https://opencitations.net/index/coci/api/v1/references/10.1371/JOURNAL.PCBI.1009105

The BioStudies database-one stop shop for all data supporting a life sciences study.

3 May 2022

1 reference

https://opencitations.net/index/coci/api/v1/references/10.1371/JOURNAL.PCBI.1009105

The metabolomics of asthma control: a promising link between genetics and disease

3 May 2022

1 reference

https://opencitations.net/index/coci/api/v1/references/10.1371/JOURNAL.PCBI.1009105

Improving lipid mapping in Genome Scale Metabolic Networks using ontologies

3 May 2022

1 reference

https://opencitations.net/index/coci/api/v1/references/10.1371/JOURNAL.PCBI.1009105

1H nuclear magnetic resonance-based metabolic profiling of cerebrospinal fluid to identify metabolic features and markers for tuberculosis meningitis

3 May 2022

1 reference

https://opencitations.net/index/coci/api/v1/references/10.1371/JOURNAL.PCBI.1009105

Evaluation and comparison of bioinformatic tools for the enrichment analysis of metabolomics data.

3 May 2022

1 reference

https://opencitations.net/index/coci/api/v1/references/10.1371/JOURNAL.PCBI.1009105

Metabolite identification: are you sure? And how do your peers gauge your confidence?

3 May 2022

1 reference

https://opencitations.net/index/coci/api/v1/references/10.1371/JOURNAL.PCBI.1009105

Proposed minimum reporting standards for chemical analysis

3 May 2022

1 reference

https://opencitations.net/index/coci/api/v1/references/10.1371/JOURNAL.PCBI.1009105

The strengths and weaknesses of NMR spectroscopy and mass spectrometry with particular focus on metabolomics research

3 May 2022

1 reference

https://opencitations.net/index/coci/api/v1/references/10.1371/JOURNAL.PCBI.1009105

Metabolomics analysis of human acute graft-versus-host disease reveals changes in host and microbiota-derived metabolites

3 May 2022

1 reference

https://opencitations.net/index/coci/api/v1/references/10.1371/JOURNAL.PCBI.1009105

Genomewide landscape of gene-metabolome associations in Escherichia coli

3 May 2022

1 reference

https://opencitations.net/index/coci/api/v1/references/10.1371/JOURNAL.PCBI.1009105

Multi-omics analysis identifies ATF4 as a key regulator of the mitochondrial stress response in mammals

3 May 2022

1 reference

https://opencitations.net/index/coci/api/v1/references/10.1371/JOURNAL.PCBI.1009105

10.1371/JOURNAL.PCBI.1009105

3 May 2022

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